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Re: [h5md-user] Subgroups

From: Felix Höfling
Subject: Re: [h5md-user] Subgroups
Date: Mon, 23 Sep 2013 14:45:39 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 09.09.2013, 12:43 Uhr, schrieb Konrad Hinsen <address@hidden>:

One of the points that are unclear to me in the current specification
is the definition of subgroups.

Suppose I have a system consisting of a protein in solvent. I want to
have two subgroups, "protein" and "solvent". But I also have data that
applies to the whole system, without breaking it down into subgroups.
And I might have yet another data set that uses different subgroups
for a specific purpose.

My understanding of the current specification is that particles
are numbered from 0 to N-1 inside each subgroup. I would have
atoms number 0 to K-1 for my protein, and 0 to L-1 for my solvent.
Then how do I know what these atoms correspond to in the complete
system? That information cannot be deduced from the data for each
subgroup, so it has to be supplied somewhere else. But where?


Hi Konrad,

It seems that your question on the subgroups has not yet been answered.

So far, the subgroups have mainly be used for output purposes not to reconstruct a complete simulation (except for a few cases with manual interference where the user has provided the semantics between the subgroups).

Actually, the intention of H5MD is that not all information has to be stored (e.g., solvent particles may be absent), in this sense the union of all subgroups does not yield the complete set of particles. On the other hand, the subgroups are not required to be disjoint subsets. For examples, subgroups may be selected according to particle type or to a region in space, which makes a lot of sense for the observable tree.

I'm not sure whether overlapping subgroups are also useful for the data in "particles". (Maybe one example for a spatial selection: a user wants to analyse the interfacial region between two liquids, so only a shallow slab along the interface is stored instead of all particles.) Do you see a problem here w.r.t. your applications?

Automatic reconstruction of a complete simulation from a H5MD file would be nice, but there is much more to it than just particle coordinates. Then, one would have to enter into specifying particle interactions in a generic way which appears impossible to me.


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